Pairwise Sequence Alignment between HBV and HCC Using Modified Needleman Wunsch Algorithm

Lailil Muflikhah, Edy Santoso

Abstract


Ths paper aims to find similarity of Hepatitis B virus (HBV) and Hepatocelluler Carcinoma (HCC) DNA sequences.The similarity of sequence allignments indicates that they have similarity of chemical and physical properties. Mutation of the virus DNA in X region has potential role in HCC. It is observed using pairwise sequence alignment of genotype-A in HBV. This paper is to purpose the modified method of Needleman Wunsch algorithm for optimum global DNA sequence alignment. The main idea is to optimize filling matrix and backtracking proccess of DNA components, so that there is reduction of computational time and space complexity. This research is applied to DNA sequence of 858 hepatitis B virus and 12 carcinoma patient. There are 10,296 pairwise of DNA sequences to be aligned globally using the modified method. As a result, it is achieved high similarity of 96.547% and validity of 99.854%. There is reduction of computational time as 34.6% and space complexity as 42.52%


Keywords


hepatitis, sequence alignment, DNA, Needleman-Wunsch, optimum global

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DOI: http://dx.doi.org/10.12928/telkomnika.v15i4.5813

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